A2 Biology Notes Cellular Respiration

A2 Biology Notes: Cellular Respiration

Cellular Respiration

1. Outline the need for energy in living organisms, as illustrated by anabolic reactions, active transport, movement and the maintenance of body temperature.

Cells use energy for many different purposes. These includea. The synthesis of proteins and the other large molecules from smaller ones.

These are examples of anabolic reactions, that is energy-consuming reactions (Anabolic reactions build new molecules and/or store energy).

b. For active transport of ions and molecules across cell membranes against the concentration gradient.

c. For transmission of nerve impulse.d. For movement, for example muscle contraction (such as heart beat,

breathing movements, walking) or movement of cilia.e. In mammals and birds, the production of heat to maintain body temperature

at a steady level.f. Activation for glycolysis of glucose wherein the molecule is energized by the

addition of phosphates. g. Light-independent reactions of photosynthesis use the ATP and NADPH

synthesized during a chemical reactions of light-dependent reactions to provide energy for the synthesis of glucose and other organic molecules from inorganic carbon dioxide and water.

2. Describe the structure of ATP as a phosphorylated nucleotide.

It consists of adenine (an organic base) and ribose (pentose sugar), which together make adenosine (a nucleotide).

Adenosine is then combined with 3 phosphate groups to make ATP (adenosine triphosphate).

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Adenosine Tri-Phosphate or more conveniently ATP, is a small molecule made of a 5 carbon ribose sugar, a nitrogenous base Adenine (a purine) and three phosphates.

It is known as a nucleotide derivative as it is very similar in structure to an RNA nucleotide. The main difference between the two is that ATP has three phosphates while the RNA nucleotide only has one phosphate.

ATP is a source of energy for all living organisms and is referred to as the Universal Energy Currency.

As ATP is used by all cells in an organism, it has a standardized process of releasing or storing energy. ATP is therefore a currency of energy that is universally used within organisms.

ATP stores its energy in high energy bonds between each of the inorganic phosphates. Energy can be released each time a phosphate is cleaved from the main ATP molecule. The energy that is released is done so in small manageable amounts, enough to carry out most metabolic reactions however not too much. Energy released in small quantities ensures there is no excess energy that will be wasted or that could physically damage cell components.

During respiration ATP can be created by using the energy from respiratory substrates (lipids, carbohydrates and proteins) to add a phosphate to ADP to create ATP and so creating a high energy bond between the two phosphates.

3. Describe the universal role of ATP as the energy currency in all living organisms.

ATP - A universal energy currency It acts as immediate donor of energy in the cell’s requiring reactions. ATP is the universal intermediary molecule between energy-yielding

reaction and energy requiring reactions used in a cell.

Properties of ATP as energy currency ATP is small, water-soluble molecule. This allows it to be easily

transported around the cell. When a phosphate groups is removed from the ATP, adenosine

diphosphate (ADP) is formed and 30.5KJ mol-1 of energy released. Removal of a second phosphate produces adenosine

monophosphate (AMP) and 30.5 KJ mol-1 of energy released. Removal of the last phosphate, leaving adenosine, releases only

14.1 KJ mol-1. These reactions are all reversible.

Energy transfers are inefficient because Some energy is converted to thermal or heat energy. Many energy-requiring reactions in cells use less energy than that

released which will change to thermal.

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4. Explain that the synthesis of ATP is associated with the electron transport chain on the membranes of the mitochondrion.

Synthesis of ATP Energy for ATP synthesis can be become available in two ways:

In respiration energy released by reorganizing chemical bond during glycolysis and Krebs cycle (chemical potential energy) is used to make ATP.

Most ATP in cells in general using electrical potential energy.

Chemiosmosis (electrical potential energy): It is the process in which ATP is generated using electrical potential

energy. The energy is from the transfer of electrons by electron carriers in

the mitochondria. Phospholipids membranes in mitochondria are impermeable to

hydrogen ions. Hydrogen ions are then allowed to flow down their concentration

gradient through protein and part of this protein acts as an enzyme which synthesizes ATP called ATP synthesis.

The flow of 3 hydrogen allows the production of one ATP molecule provided that ADP and inorganic phosphate group (Pi) are available inside the organelles.

ATP synthesis has 3 binding sites and a part of the molecules that rotates as hydrogen ion pass, this produce structural changes and allow them to pass sequentially through 3 phase: a) binding ATP and (Pi), b) forming tightly bound ATPc) releasing ATP

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Shows the breakdown of ATP releases energy for powering

cellular activities in organisms


5. Outline glycolysis as phosphorylation of glucose and the subsequent splitting of hexose phosphate (6C) into two triose phosphate molecules, which are then further oxidized with a small yield of ATP and reduced NAD.

The word glycolysis means ‘sugar splitting’ and is thought to have been one of the first biochemical pathways to evolve. It uses no oxygen and occurs in the cytosol of the cell. There are no required organelles. The sugar splitting proceeds efficiently in aerobic and anaerobic environments. Glycolysis occurs in both prokaryotic and eukaryotic cells. A hexose, usually glucose, is split in the process. This splitting actually involves many steps but we can explain it effectively in three stages.

Three Stages of Glycolysis

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First: Two molecules of ATP are used to begin glycolysis. In the first reaction, the phosphates from the ATPs phosphorylate glucose to form fructose-1, 6-biphosphate. This process involves phosphorylation.


Summary

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Second: The 6-carbon phosphorylated fructose is split into two 3-carbon sugars called glyceraldehydes-3-phosphate (G3P). This process involves lysis.

Third: Once the two G3P molecules are formed, they enter an oxidation phase involving ATP formation and production of the reduced coenzyme NAD. Each G3P or triose phosphate molecule undergoes oxidation to form a reduced molecule of NAD+, which is NADH. As NADH is being formed, released energy is used to add an inorganic phosphate to the remaining 3-carbon compound. This results in a compound with two phosphate groups. Enzymes then remove the phosphate groups so they can be added to ADP to produce ATP. The end result is the formation of 4 molecules of ATP, 2 molecules of NADH, and 2


NAD+ is an electron carrier molecule that helps pass energy from glucose to other pathways in a cell by taking high-energy electrons and holding on to them until they can be transferred to other molecules.

6. Explain that, when oxygen is available, pyruvate is converted into acetyl (2C) coenzyme A, which then combines with oxaloacetate (4C) to form citrate (6C).

Link reaction: Pyruvate passes by active transport from the cytoplasm, through the outer

and inner membranes of the mitochondria and into the mitochondrial matrix.

Here it is decarboxylated (that’s when CO2 is removed), dehydrogenated and combined with coenzyme A (COA) to give acetyl coenzyme A.

Coenzyme A acts as a carrier of acetyl groups in the Krebs cycle.

7. Outline the Krebs cycle, explaining that citrate is reconverted to oxaloacetate in a series of small steps in the matrix of the mitochondrion (no further details are required).

Once glycolysis has occurred and there is oxygen present, pyruvate enters the matrix of the mitochondrion via active transport. Inside, pyruvate is decarboxylated to form the 2-carbon acetyl group. This is the link reaction. The removed carbon is released as CO2, a waste gas. The acetyl group is then oxidized with the formation of reduced NAD+. Finally, the acetyl group combines with coenzyme A (CoA) to form acetyl CoA.

The Link Reaction: Controlled by a system of enzymes. The greatest significance of this reaction is that it produces acetyl CoA. Acetyl CoA may enter the Krebs cycle to continue the aerobic respiration process.

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Summary of glycolysis Two ATPs are used to start the

process. A total of 4 ATPs are produced –a net

gain two ATPs. Two molecules of NADH are

produced.w0/chapter25/animation__how_glycolysis_works.html

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_glycolysis_works.html




If cellular ATP levels are low, the acetyl CoA enters the Krebs cycle. This cycle is also called the tricarboxylic acid cycle. It occurs in the matrix of the mitochondrion and is referred to as a cycle because it begins and ends with the same substance. This is a characteristic of all cyclic pathways in metabolism. You do not meet to remember the names of all compounds formed in the Krebs cycle. However, it is important that you understand the overall process.

Let’s consider the cycle as a series of steps.1. Acetyl CoA from the link reaction combines with a 4-carbon compound

called oxaloacetate. The result is a 6-carbon compound called citrate.

2. Citrate (6-carbon compound) is oxidized to form a 5-carbon compound. In this process, the carbon is released from the cell (after combining with oxygen) as carbon dioxide. While the 6-carbon compound is oxidized, NAD+

is reduced to form NADH.

3. The 5-carbon compound is oxidized and decarboxylated to form a 4-carbon compound. Again, the removed carbon combines with oxygen and is released as carbon dioxide. Another NAD+ is reduced to form NADH

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Acetyl CoA combines with oxaloacetate to form citrate

Then a 5-carbon compound is formed


4. The 4-carbon compound undergoes various changes resulting in several products. One product is another NADH. The coenzyme FAD is reduced to form FADH2. There is also a reduction of an ADP to form ATP. The 4-carbon compound is changed during these steps to re-form the starting compound of the cycle, oxaloacetate. The oxaloacetate may then begin the cycle again.

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Next, a 4-carbon compound is produced.

Finally, the 4-carbon compound is converted to oxaloacetate


Summary of Krebs Cycle

It is important to remember that the Krebs cycle will run twice for each glucose molecule entering cellular respiration. This is because a glucose molecule forms 2 pyruvate molecules. Each pyruvate produces one acetyl CoA which enters the cycle. Look again at the complete Krebs cycle and note the following products which result from the breakdown of one glucose molecule:

a. 2 ATP moleculesb. 6 molecules of NADH (allow energy storage and transfer)c. 2 molecules of FADH2d. 4 molecules of carbon dioxide (released)

So far, only 4 ATPs have been gained: 6 are generated (4 from glycolysis and 2 from the Krebs cycle) but two are used to start the process of glycolysis. Each of these ATPs has been produced by substrate-level phosphorylation.Ultimately, the breakdown of each glucose molecule results in a net gain of 36 ATPs. Let’s now consider the phase of cellular respiration where most of the ATPs are produced. In this phase, oxidative phosphorylation is the means by which the ATPs are produced.

CHECK THIS WEBSITE FOR REFERENCEAnimation for Glycolysis. Krebs cycle and electron transport chainhttp://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_krebs_cycle_works__quiz_1_.html

8. Explain that these processes involve decarboxylation and dehydrogenation and describe the role of NAD.

Decarboxylation – removal of carbon from a molecule forming CO2Dehydrogenation – removal of hydrogenNAD – can accept hydrogen (reversible) to form reduced NAD (NADH2)

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http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_krebs_cycle_works__quiz_1_.html

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_krebs_cycle_works__quiz_1_.html


NAD+ is an electron carrier molecule that helps pass energy from glucose to other pathways in a cell by taking high-energy electrons and holding on to them until they can be transferred to other molecules.

Nicotinamide adenine dinucleotide ( NAD) serves as an electron acceptor in the metabolic pathway known as glycolysis . When NAD accepts its electrons it also acquires a proton (H+)and is converted into NADH. NADH is a reduced electron carrier.

NAD and FAD become NADH and FADH2respectively, this is because they become electron carriers. This happens in the breakdown of Acetyl CoA in the Krebs cycle (aka the citric acid cycle) inside the second membrane of the mitochondria. NADH and FADH2 will carry and donate the electrons to the Electron Transport Chain on the internal membrane; the transfer of the electron's energy allows for the proteins crossing the membrane to pump hydrogen ions into the space between the two membranes and build up a gradient for chemiosmosis. The NADH and FADH2becomes NAD and FAD again and returns to the Krebs cycle.

NADH then becomes oxidized in the first step of electron transport by mitochondrial complex I or NADH dehydrogenase. NADH contains flavin mononucleotide (FMN) as a bound prosthetic group, which is responsible for catalyzing the reaction.

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9. Outline the process of oxidative phosphorylation, including the role of oxygen (no details of the carriers are required).

Animation:http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__electron_transport_system_and_atp_synthesis__quiz_1_.html

a. The hydrogen picked up by NAD and FAD (in glycolysis 2NADH, Link reaction 2NADH, Krebs cycle 6 NADH and 2 FADH2) SPLITS by a dehydrogenase enzymes into electrons and proton.

b. The electrons are passed along the ETC on the inner membrane of the mitochondrion.

c. As the electrons move along the chain, they lose energy. This energy is used to actively transport hydrogen ions (proton) from the matrix of the mitochondrion across the inner membrane (cristae) and into the space between the inner and outer membrane.

d. The movement of hydrogen ions (proton) in an intermembrane space builds up an electrochemicalgradient or chemiosmosis.

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http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__electron_transport_system_and_atp_synthesis__quiz_1_.html


e. The hydrogen ions (proton) are allowed to diffuse back into the matrix through ATPases (a channel in the cristae that transport protons back to the matrix) which will provide energy to make ADP combine with inorganic phosphate to form ATP.

f. Then the electrons that are previously split by a dehydrogenase enzyme reunites and combine with oxygen to produce water. Oxygen is the final acceptor for the hydrogen removed from the respiratory substrate during glycolysis, link reaction and Krebs cycle.

10. Explain the production of a small yield of ATP from anaerobic respiration and the formation of ethanol in yeast and lactate in mammals, including the concept of oxygen debt.

Anaerobic respirationIf oxygen is not available, oxidative phosphorylation cannot take place, as there is nothing to accept the electrons and protons at the end of the electron transport chain. This means that reduced NAD is not reoxidised, so the mitochondrion quickly runs out of NAD and FAD that can accept hydrogen from the Krebs cycle reactions. The Krebs cycle and the link reaction therefore come to a halt.

Glycolysis can still continue so long the pyruvate produced at the end of it can be removed and the reduced NAD can be converted back to NAD.

The lactate pathway

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Location: cytoplasm

Substrate: Glucose

Product: lactic acid (lactate) + ATP

Note: lactic anaerobic respiration supplements aerobic respiration in the production of ATP. Both aerobic and anaerobic respiration can take place in the human cell at the same time.

The lactate that is produced (usually in muscles) diffuses into the blood and is carried in solution in the blood plasma to the liver. Here, liver cells convert it back to pyruvate. This requires oxygen, so extra oxygen is required after exercise has finished. The extra oxygen is known as the oxygen debt. Later when the exercise has finished and oxygen is available again, some of the pyruvate in the liver cells is oxidized through the link reaction, the Krebs cycle and the electron transport chain. Some of the pyruvate is reconverted to glucose in the liver cells. The glucose may be released into the blood or converted to glycogen and stored.

The ethanol PathwayIn yeast and in plants, the pyruvate is removed by converting it to ethanol.

Location: cytoplasm

Substrate: Glucose

Product: Ethanol + carbon dioxide + ATP

This is the end point for this fermentation reaction. Ethanol and CO2are both excreted with no further metabolism of the energy stored in the ethanol (very inefficient)

Note: The glucose molecule has been hydrolysed further than in human respiration. Some organisms are totally anaerobic others can switch between anaerobic and aerobic.

Fermentation respiration in yeast yields two useful products from a human perspective. The carbon dioxide can be used in a variety industrial processes the best known of which is to raise bread. Many Brewers of alcohol will bottle the CO2 for use in the 'carbonation' of other drink products.

The alcohol itself is of course the basis of many industries such as beer brewing. In more recent time the use of fermentation products is being used as an alternative source of fuel such as is the case in fuel for automobiles.

ATP yield in aerobic and anaerobic respiration

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Only small amounts of ATP are produced when one glucose molecule undergoes anaerobic respiration. This is because only glycolysis is completed. The Krebs cycle and oxidative phosphorylation, which produce most ATP, do not take place.The precise number of molecules of ATP produced in aerobic respiration of one glucose varies between different organisms and different cells, but is usually between 30 and 32 molecules

11. Explain the relative energy values of carbohydrate, lipid and protein as respiratory substrates.

The greater number of hydrogen present, the greater the energy value. Lipids have higher energy density than carbohydrates.Could use a calorimeter to burn substances to compare the rise in temperature.

The more hydrogens, the more ATP is produced in the electron transport chain

Some molecules have more hydrogens than others The more hydrogen atoms there are in a respiratory substrate, the more

ATP is produced If there are more hydrogen atoms per mole (fixed amount) of substrate, the

more oxygen is needed to be the final acceptor

Energy values of different respiratory substratesRespiratory substrate Energy released/kJg-1Carbohydrates 16Lipid 39Protein 17

Lipid provides more than twice as much as energy per gram as carbohydrate or protein. This is because of lipid molecule contains relatively more hydrogen atoms (in comparison with carbon or oxygen atoms) than carbohydrate or protein molecules do. It is hydrogen that are used to generate ATP via the electron transport chain

12. Define the term (l) respiratory quotient (RQ).

Respiratory quotient – is the ratio of the volume of carbon dioxide released to the volume of oxygen consumed by a body tissue or an organism in a given period.

Note: if RQ of animal is 0.9 - mainly suggest that the animal is metabolizing protein molecule.Lipid RQ: 0.7Glucose: 1

13. [PA] Carry out investigations, using simple respirometers, to measure RQ and the effect of temperature on respiration rate.

Respirometer measures volume of oxygen used by organism

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Soda lime absorbs carbon dioxide produced by aerobic respiration. Volume of oxygen used is measured in manometer capillary tube. Measure distance travelled by meniscus over time. As area of capillary tube

is known, can calculate mean rate of oxygen uptake in mm3min-1

Important to equilibrate equipment/organism to temperature Use a control to make sure differences not due to temperature/pressure If testing plants, then need to be in dark to prevent photosynthesis.

Dehydrogenase - an enzyme that catalyzes the removal of hydrogen from a substrate and the transfer of the hydrogen to an acceptor in an oxidation-reduction reaction.

Lab bench on respiration

http://www.phschool.com/science/biology_place/labbench/lab5/features.html

Practical Activity

Measuring respiratory quotient

The purpose of this activity is:

to use a respirometer to measure the oxygen uptake of some respiring plant or animal material

to use the respirometer again to measure the net volume of gas exchanged by the respiring material and hence calculate the volume of carbon dioxide given out by the material

to calculate the respiratory quotient (RQ) for the respiring material

to use the RQ as evidence of the respiratory substrate in use

Procedure Potassium hydroxide and soda lime are corrosive. Wear goggles when handling and seek first aid immediately if any gets in your eyes.

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Push the parts of the equipment together firmly but gently to get airtight seals, but reduce the risk of breaking any glass apparatus and injuring yourself.

Preparationa Use a funnel to pour 5 cm3 of potassium hydroxide solution (corrosive)

into each respirometer vessel. Make sure none of the potassium hydroxide touches the sides of the vessels.

b Add small rolls of filter paper to act as wicks.

c Fill the basket or cage with respiring material and put it into vessel B. Make sure that the seeds or invertebrates are not touching the potassium hydroxide or the wick. Add water to vessel A to match the volume of respiring material in vessel B (see diagram overleaf).

d Fit vessel A with a bung holding two connecting tubes – one with a screw clip on flexible tubing. Alternatively fit a bung with a 3-way tap connected to the same items.

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e Fit vessel B with a bung holding a 1 cm3 syringe and a connecting tube as shown in the diagram. Alternatively fit a bung with a 3-way tap connected to the syringe and tube.

f Draw some coloured fluid into the manometer U-tube. The fluid must be free of bubbles and come to about the middle of the scale on each side.

g Open the screw clip and remove the syringe, then connect the manometer U-tube. To check that the apparatus is airtight, move the marker fluid in the manometer to one end with the syringe and leave for a few minutes. The fluid should not move.

h Set the piston of the syringe at about the 0.5 cm3 mark and insert the syringe as shown. Close the screw clip. Use the syringe to adjust the manometer so that the fluid levels are the same on both sides.

i Record the exact position of the syringe piston, the position of the menisci on both sides of the manometer, and the time.

Investigationj Record new positions of the manometer fluid at regular intervals for 30

minutes. When it nears the end of the scale on one side, restore it to its original position and note the new position of the syringe piston.

k Find the amount of oxygen absorbed by germinating seeds in a period of 30 minutes at 20 °C. This is Vol1.

l Remove the potassium hydroxide solution from both vessels and wash them out with water.

m Replace the basket containing seeds or invertebrates in one vessel, an equivalent volume of water in the other vessel and the bungs in both. Set up the respirometer a 20 °C again and record any increase or decrease in gas volume over the next 30 minutes. This is Vol2.

n Calculate the volume of carbon dioxide produced.

o Calculate the respiratory quotient.

REMINDERS:17


Using 2 -3 different organisms - They should be the same in mass, conduct the experiment in

a temperature-controlled room (air-conditioned room).- If handling algae or pond weed - keeping them in a

container and in the dark. Always include RISK ASSESSMENT in your written procedure. You may include the use of thermostatically controlled water

bath to maintain temperature. A change in temperature will cause a direct change in volume.

Because the temperature in the respirometersmay vary during the course of the experiment, you must correct for differences in volume that are due to temperature fluctuation rather than rate of respiration. To do this, subtract any difference in the movement of water into the vial with glass beads from the experimental vials held at the same temperature. Record the result as the corrected difference.

Ensure apparatus is airtight Mention the word REPEAT or REPLICATE at least 3 times. You can also provide control in your experiment by using a

dead organism or a glass beads for comparison

How to calculate the rate of respiration (oxygen uptake)

http://www.phschool.com/science/biology_place/labbench/lab5/measure.html

After you have collected data for the amount of oxygen consumed over time by germinating and nongerminating peas at two different temperatures, you can compare the rates of respiration. Let's review how to calculate rate.

Rate = slope of the line, or

In this case, Δ y is the change in volume, and Δ x is the change in time (10 min).

Or divide volume by mass or divide O2 by time.

How to calculate rate of respiration or oxygen uptakeCollect the date by taking the diameter of the capillary tube and its volume.Divide volume with its diameter then multiply with the distance travelled by the water/ air or dye in the capillary tube in a given time.OrDivide volume of O2 by mass to give you the unit cm3/g

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Or Divide of O2 by time to give you the unit cm3/minOrVolume of O2 divided by time times mass = cm3 s-1 g-1

How to calculate the rate of carbon dioxideWeigh the CO2 absorbent before and after the experimentCalculate the differenceDivide the difference in distance over volume by time

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A2 Biology: Cellular Respiration Anglo Singapore International School

QUESTIONS

1 Use this table to record your results and guide your calculations. Compare your results with those of others in your class.

Net volume change in 30 minutes with

carbon dioxide absorbed = oxygen

taken in

Net volume change in 30

minutes with no CO2 absorbed

Amount of carbon dioxide absorbed

Respiratory quotient =

(carbon dioxide produced)/

(oxygen absorbed)

Vol1 Vol2 Vol1 + Vol2 (Vol1 + Vol2) / Vol1

2 What respiratory substrate would you expect to find in seeds?

3 Does your value for RQ support your thinking?

4 What tests can you think of that would allow you to find out what substrates are present?

5 What would you expect to be the RQ of a growing culture of yeast?

6 Suggest three different explanations for respiring material in this test producing an RQ of 1.0.

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A2 Biology: Cellular Respiration Anglo Singapore International School

ANSWERS

1 Calculations: this will depend on experimental results.

2 Seeds such as sunflower contain oils. Other seeds contain more carbohydrates. All contain proteins – raw materials for the initial growth of seedlings.

3 An RQ value around 0.7 is what you would expect for oils.

4 You could carry out standard food tests to confirm the components of seeds. To test for oils: Crush the seeds and shake with about 1 cm3 of ethanol. Use a pipette to collect some of the ethanol and drip into water. If the water becomes cloudy as an emulsion forms, this suggests the presence of oils or fats in the seeds. To test for starch: crush a couple of seeds and add to a drop of iodine solution on a dimple tile. A blue-black colour indicates the presence of starch.

5 If the yeast culture is growing rapidly and respiring anaerobically, it will take in very little oxygen and so the RQ will be very large and effectively meaningless.

6 Three explanations for respiring material in this test producing an overall RQ of 1.0 are:

aerobic respiration of a carbohydrate substrate,

aerobic respiration of two substrates together – one with an RQ above 1.0 and the other with an RQ below 1.0,

aerobic respiration of a substrate with a respiratory quotient less than 1.0 and anaerobic respiration of another substrate.

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A2 Biology Notes Cellular Respiration